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| The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file. | | The <code>stats</code> option on the [[BamUtil]] executable generates the specified statistics on a SAM/BAM file. |
| + | |
| + | = Usage = |
| + | <pre> |
| + | ./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>][--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--sumStats] [--noeof] [--params] |
| + | </pre> |
| + | |
| | | |
| = Parameters = | | = Parameters = |
− | <pre> Required Parameters: | + | <pre> |
− | --in : the SAM/BAM file to calculate stats for | + | Required Parameters: |
| + | --in : the SAM/BAM file to calculate stats for |
| Types of Statistics that can be generated: | | Types of Statistics that can be generated: |
− | --basic : Turn on basic statistic generation | + | --basic : Turn on basic statistic generation |
− | --qual : Generate a count for each quality (displayed as non-phred quality) | + | --qual : Generate a count for each quality (displayed as non-phred quality) |
− | --phred : Generate a count for each quality (displayed as phred quality) | + | --phred : Generate a count for each quality (displayed as phred quality) |
− | --baseQC : Write per base statistics to the specified file. | + | --baseQC : Write per base statistics to the specified file. |
| Optional Parameters: | | Optional Parameters: |
− | --maxNumReads : Maximum number of reads to process | + | --maxNumReads : Maximum number of reads to process |
| Defaults to -1 to indicate all reads. | | Defaults to -1 to indicate all reads. |
− | --unmapped : Only process unmapped reads (requires a bamIndex file) | + | --unmapped : Only process unmapped reads (requires a bamIndex file) |
− | --bamIndex : The path/name of the bam index file | + | --bamIndex : The path/name of the bam index file |
| (if required and not specified, uses the --in value + ".bai") | | (if required and not specified, uses the --in value + ".bai") |
− | --regionList : File containing the region list chr<tab>start_pos<tab>end<pos>. | + | --regionList : File containing the regions to be processed chr<tab>start_pos<tab>end<pos>. |
| Positions are 0 based and the end_pos is not included in the region. | | Positions are 0 based and the end_pos is not included in the region. |
| Uses bamIndex. | | Uses bamIndex. |
− | --minMapQual : The minimum mapping quality for filtering reads in the baseQC stats. | + | --minMapQual : The minimum mapping quality for filtering reads in the baseQC stats. |
− | --dbsnp : The dbSnp file of positions to exclude from baseQC analysis. | + | --dbsnp : The dbSnp file of positions to exclude from baseQC analysis. |
− | --noeof : Do not expect an EOF block on a bam file. | + | --noeof : Do not expect an EOF block on a bam file. |
− | --params : Print the parameter settings | + | --params : Print the parameter settings |
| + | Optional Base QC Only Parameters: |
| + | --sumStats : Alternate summary output. |
| </pre> | | </pre> |
| For all types of statistics, the bam file used is specified by <code>--in</code>. | | For all types of statistics, the bam file used is specified by <code>--in</code>. |
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| The optional parameters are also used for all types of statistics. | | The optional parameters are also used for all types of statistics. |
| | | |
− | Usage:
| |
− | <pre> ./bam stats --in <inputFile> [--basic] [--qual] [--phred] [--baseQC <outputFileName>] [--maxNumReads <maxNum>] [--unmapped] [--bamIndex <bamIndexFile>] [--regionList <regFileName>] [--minMapQual <minMapQ>] [--dbsnp <dbsnpFile>] [--noeof] [--params]
| |
− | </pre>
| |
− | <br>
| |
| | | |
| = Types of Statistics = | | = Types of Statistics = |